I went to update my Gentoo installation after a few months of humming along, and quite unexpectedly found it was trying to install xorg (I run a text-only server). I've seen recent complaints about incorrect dependencies on Gnome, but nothing regarding this (the one thread I did post on was moved to duplicate threads before anything could come of it).

X is fairly pervasive, keeping it out of your install can be difficult. I'd install ufed and go through the entire list, and remove anything you don't need.

When you do run into these cases where something's getting installed in an emerge -uD world, you can go through the whole list of packges and emerge -ptv them all, to narrow down which package is causing it to be installed. Once you figure out which package is causing it, do trial and error via 'USE="-flag" emerge -pv package' until you figure out which flag is bad.